I use a 383L with fiter wheel and DSS to register and stack the images.
I set up DSS like this:
- Load all the light frames, bias, darks and flats.
- Set one light frame as the reference for registering. This is the important thing.
- Select the frames required for one fiter - that's the darks and bias frames but only the lights and flats for that filter.
- Save this file list with a name that reflects the filter, such as lovejoy-R
- Unselect the lights and flats, select those for another filter and save that file list.
- Do this for all filters.
Use Batch Stacking and select the file lists you set up above.
Start it, go and do something else until it's finished.
You end up with fits or tiff files of the processed, registered and stacked images. They all use the same reference image so are all stacked correctly.
I handle the image processing separately, the important thing is that because they all use the same reference image the processed images are correctly registered.
Hope this helps,
Chris.